3J1P

Atomic model of rabbit hemorrhagic disease virus

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EGT
experimental model	PDB	4EJR

Sample
Wild Rabbit Hemorrhagic Disease Virus (strain HYD)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 3 seconds before plunging into liquid ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	26000
Reported Resolution (Å)	6.5
Resolution Method	FSC 0.5 CUT-OFF
Other Details	The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom (details about the particle: the particles were selec ...	The final map was sharpened to 4.5 Angstrom with B factor -300 and then filtered to 5.0 Angstrom (details about the particle: the particles were selected using an automatic selection program FindEM).
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (4EGT)	2 (4EJR)	3
Refinement Space	REAL	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	FLEXIBLE FIT	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The P domains were separately fitted into the map by automatic ...	REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The P domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).	REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The S domains were separately fitted into the map by automatic ...	REFINEMENT PROTOCOL--symmetry restrained molecular dynamics flexible fitting DETAILS--The S domains were separately fitted into the map by automatic rigid body fitting using Chimera (FIT IN MAP).	REFINEMENT PROTOCOL--Manual building of NTA domain DETAILS--The N-terminal NTA domain was manually built according to the high resolution EM map.

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2011-01-22
Temperature (Kelvin)	85
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	96000
Calibrated Magnification	160770
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Coot
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	1.9
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF correction of each whole micrograph

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.